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- PDB-4uox: Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate ... -

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Basic information

Entry
Database: PDB / ID: 4uox
TitleCrystal structure of YgjG in complex with Pyridoxal-5'-phosphate and putrescine
ComponentsPUTRESCINE AMINOTRANSFERASE
KeywordsTRANSFERASE / POLYAMINE
Function / homology
Function and homology information


diamine transaminase / putrescine-2-oxoglutarate transaminase / diamine transaminase activity / putrescine--2-oxoglutarate transaminase activity / L-lysine catabolic process / putrescine catabolic process / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Putrescine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Putrescine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / 1,4-DIAMINOBUTANE / Putrescine aminotransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.085 Å
AuthorsJeong, J.H. / Kim, Y.G.
CitationJournal: Plos One / Year: 2014
Title: Structure of Putrescine Aminotransferase from Escherichia Coli Provides Insights Into the Substrate Specificity Among Class III Aminotransferases.
Authors: Cha, H.J. / Jeong, J. / Rojviriya, C. / Kim, Y.
History
DepositionJun 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTRESCINE AMINOTRANSFERASE
B: PUTRESCINE AMINOTRANSFERASE
C: PUTRESCINE AMINOTRANSFERASE
D: PUTRESCINE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,05321
Polymers203,1414
Non-polymers1,91217
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33680 Å2
ΔGint-201.7 kcal/mol
Surface area52120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.124, 129.520, 131.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PUTRESCINE AMINOTRANSFERASE / YGJG / PUTRESCINE--2-OXOGLUTARIC ACID TRANSAMINASE / PAT / PATASE


Mass: 50785.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: COVALENT BOND BETWEEN PYRIDOXAL-5'-PHOSPHATE AND PUTRESCINE
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P42588, putrescine-2-oxoglutarate transaminase

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Non-polymers , 6 types, 530 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12N2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE (PLP): PYRIDOXAL-5'-PHOSPHATE IS COVALENTLY BOUND WITH PUTRESCINE IN CHAIN ...PYRIDOXAL-5'-PHOSPHATE (PLP): PYRIDOXAL-5'-PHOSPHATE IS COVALENTLY BOUND WITH PUTRESCINE IN CHAIN A,B. 1,4-DIAMINOBUTANE (PUT): PYRIDOXAL-5'-PHOSPHATE IS COVALENTLY BOUND WITH PUTRESCINE IN CHAIN A,B.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.65 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 15% PEG 3350, 0.2 M SODIUM FORMATE, 0.1 MM N-DODECYL-N,N-DIMETHYLGLYCINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 123102 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 21.07 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.4 / % possible all: 81.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VEF

1vef


Resolution: 2.085→36.257 Å / SU ML: 0.29 / σ(F): 1.5 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 5528 5.1 %
Rwork0.1875 --
obs0.1905 109557 88.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.085→36.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13759 0 123 513 14395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814127
X-RAY DIFFRACTIONf_angle_d1.17219091
X-RAY DIFFRACTIONf_dihedral_angle_d15.2655201
X-RAY DIFFRACTIONf_chiral_restr0.0422166
X-RAY DIFFRACTIONf_plane_restr0.0052490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.085-2.10870.31591600.29512906X-RAY DIFFRACTION76
2.1087-2.13350.32541470.28763222X-RAY DIFFRACTION82
2.1335-2.15950.35621590.26583145X-RAY DIFFRACTION81
2.1595-2.18680.28911500.25793127X-RAY DIFFRACTION81
2.1868-2.21560.30961630.27063044X-RAY DIFFRACTION79
2.2156-2.2460.33971960.28893510X-RAY DIFFRACTION91
2.246-2.2780.32251900.27023444X-RAY DIFFRACTION89
2.278-2.3120.32541790.26122900X-RAY DIFFRACTION76
2.312-2.34820.33581710.25633192X-RAY DIFFRACTION82
2.3482-2.38660.32091780.24353274X-RAY DIFFRACTION85
2.3866-2.42780.33061850.22653287X-RAY DIFFRACTION85
2.4278-2.47190.28031730.2113327X-RAY DIFFRACTION86
2.4719-2.51950.28671840.21093362X-RAY DIFFRACTION87
2.5195-2.57090.28211720.20913377X-RAY DIFFRACTION87
2.5709-2.62680.2782040.20253407X-RAY DIFFRACTION88
2.6268-2.68780.27331840.19573377X-RAY DIFFRACTION88
2.6878-2.7550.26271750.19083498X-RAY DIFFRACTION89
2.755-2.82950.25171760.19413493X-RAY DIFFRACTION90
2.8295-2.91270.27841970.19333474X-RAY DIFFRACTION90
2.9127-3.00670.24311670.20233557X-RAY DIFFRACTION91
3.0067-3.11410.2941830.19553614X-RAY DIFFRACTION92
3.1141-3.23870.24881890.18713647X-RAY DIFFRACTION93
3.2387-3.3860.24342040.18053699X-RAY DIFFRACTION95
3.386-3.56440.21012050.17773773X-RAY DIFFRACTION96
3.5644-3.78750.23592120.15953886X-RAY DIFFRACTION99
3.7875-4.07960.20921950.14573767X-RAY DIFFRACTION95
4.0796-4.48940.1691620.1263865X-RAY DIFFRACTION97
4.4894-5.13750.17072250.1283823X-RAY DIFFRACTION97
5.1375-6.46670.19412160.1553928X-RAY DIFFRACTION98
6.4667-36.26230.18482270.14154104X-RAY DIFFRACTION98

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